RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions

The high affinity and specificity of nucleic acid base complementarity has been proven to be a powerful method for constructing specific molecular assemblies. On the other hand, recent structural studies of RNA have revealed the wide range of tertiary interactions utilized in RNA folding, which may potentially be used as tools for the design of specific macromolecular assemblies. Here, RNA building blocks containing two hairpin loops, based on the dimerization initiation site (DIS) of HIV RNA, connected by a short linker were used to construct large RNA assemblies through hairpin loop-loop ("kissing") interactions. We show that specific linear and circular assemblies can be constructed in a magnesium-dependent manner using several non-self-complementary loop-loop interactions designed in this study. These results show that the use of RNA tertiary interactions may broaden the repertoire of nucleic acid-based nanostructures.